PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC25548_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family MYB
Protein Properties Length: 325aa    MW: 36990.9 Da    PI: 9.3901
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC25548_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding52.79.8e-1783128147
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                      rg W + Ed +l+++v+q+G+ +W+ Iar++  gR++k+c++rw++ 
      RrC25548_p1  83 RGHWRPTEDAKLKELVAQFGPQNWNVIARHLL-GRSGKSCRLRWFNQ 128
                      899****************************9.***********996 PP
2Myb_DNA-binding51.32.8e-16136178246
                      SSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   2 grWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                       ++T+eE+ +l+ +++ +G++ W++I+r ++ gRt++ +k++w+ 
      RrC25548_p1 136 RAFTEEEESRLLAVHRAYGNK-WALISRLFP-GRTDNAVKNHWHV 178
                      689******************.*********.***********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129415.94478129IPR017930Myb domain
SMARTSM007174.5E-1482131IPR001005SANT/Myb domain
SuperFamilySSF466895.24E-2883176IPR009057Homeodomain-like
PfamPF002491.3E-1583128IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.602.1E-2584136IPR009057Homeodomain-like
CDDcd001671.54E-1286127No hitNo description
PROSITE profilePS5129425.153130184IPR017930Myb domain
SMARTSM007173.2E-14134182IPR001005SANT/Myb domain
PfamPF002499.9E-14136177IPR001005SANT/Myb domain
CDDcd001672.67E-10137177No hitNo description
Gene3DG3DSA:1.10.10.605.5E-20137183IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051782Biological Processnegative regulation of cell division
GO:0071367Biological Processcellular response to brassinosteroid stimulus
GO:0005634Cellular Componentnucleus
GO:0001046Molecular Functioncore promoter sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 325 aa     Download sequence    Send to blast
MNQNLLKKNL TGNYTINDSR RFQERNNFRS LPNSDTNFSL ARNYPHNKSV SGLESGDEHG  60
KERGGNGLKR RGKNGINSKL CSRGHWRPTE DAKLKELVAQ FGPQNWNVIA RHLLGRSGKS  120
CRLRWFNQLD PRINKRAFTE EEESRLLAVH RAYGNKWALI SRLFPGRTDN AVKNHWHVIM  180
SRRTRESQRQ RQVQASQEPS GNAEIIVSSS CRYNHGEFSG TVANGNVFNE EDDDGDDEDA  240
SALSTCTTEL SLTPPSSTHQ ARFLNYDNTL DPGKDGQCVQ RAEVNGKYSK KMDHQNHHTI  300
TVSEERKVEM QSCFYFFDFL GVGAT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1gv2_A6e-32831844105MYB PROTO-ONCOGENE PROTEIN
1h88_C9e-327118447159MYB PROTO-ONCOGENE PROTEIN
1h89_C9e-327118447159MYB PROTO-ONCOGENE PROTEIN
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtActs as a cell-specific local repressor of quiescent center (QC) self-renewal by cell divisions in the primary root. Counteracts brassinosteroid (BR)-mediated cell division in the QC cells (PubMed:24981610). Regulates maternally seed size, especially before the heart stage, promoting both endothelial cells expansion and cell number in the outer integument layer of the seed coat (PubMed:23911125). Modulates the expression of genes involved in cell wall metabolism such as cell division and expansion (PubMed:23911125, PubMed:24981610). Negative regulator of flowering via the repression of FT transcription (PubMed:25343985). {ECO:0000269|PubMed:23911125, ECO:0000269|PubMed:24981610, ECO:0000269|PubMed:25343985}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00516DAPTransfer from AT5G17800Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Levels follow a circadian cycle with a progressive decrease during the day time (at protein level) (PubMed:25343985). Down-regulated by brassinosteroids (BRs) in a dose- and time-dependent manner. Repressed by BES1. Auto-activation of expression (PubMed:24981610). Targeted to 26S proteasomal degradation by the CULLIN3 (CUL3)-based E3 ligases CRL3(BPMs) (PubMed:25343985). {ECO:0000269|PubMed:24981610, ECO:0000269|PubMed:25343985}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018443078.10.0PREDICTED: transcription factor MYB21
SwissprotQ6R0531e-165MYB56_ARATH; Transcription factor MYB56
TrEMBLA0A3P6DEU80.0A0A3P6DEU8_BRACM; Uncharacterized protein
STRINGBra002107.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM99771836
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G17800.11e-130myb domain protein 56
Publications ? help Back to Top
  1. Chen L,Bernhardt A,Lee J,Hellmann H
    Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases.
    Mol Plant, 2015.
    [PMID:25343985]
  2. Frigola D,Caño-Delgado AI,Ibañes M
    Methods for Modeling Brassinosteroid-Mediated Signaling in Plant Development.
    Methods Mol. Biol., 2017. 1564: p. 103-120
    [PMID:28124249]
  3. Espinosa-Ruiz A, et al.
    TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana.
    Development, 2017. 144(9): p. 1619-1628
    [PMID:28320734]
  4. Jeong CY, et al.
    AtMyb56 Regulates Anthocyanin Levels via the Modulation of AtGPT2 Expression in Response to Sucrose in Arabidopsis.
    Mol. Cells, 2018. 41(4): p. 351-361
    [PMID:29487277]